Purpose

This repository contains all the data, functions, scripts to run simulations and analysis, and scripts to generate plots for the paper "Exponential-family embedding with application to cell developmental trajectories for single-cell RNA-seq data".

Installation

This package can be installed through devtools in R.

library("devtools")
devtools::install_github("linnylin92/esvd", subdir = "eSVD")

The package itself depends on several packages. These include MASS', foreach', doMC', princurve', igraph', clplite', softImpute', NMF', and plot3D' Warning: On Windows, to install the doMC` package, use the following code in R.

install.packages("doMC", repos="http://R-Forge.R-project.org")

See: http://stackoverflow.com/questions/16453625/package-domc-not-available-for-r-version-3-0-0-warning-in-install-packages

The above installation is only for the R package. To reproduce the entire simulation and analysis, you will need to pull/fork this entire repository. You will need to install the Git Large File Storage system to do this (see below).

Data

The dataset used in this article is also included in the repository. This is the Marques single-cell dataset collected by Marques et al. (2016). While the original dataset is publicly available on GEO (\url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75330}), we provide a locally preprocessed dataset, which was created to be amendable for our analysis in R. This dataset is a 21 MB .RData file, and is synced onto GitHub using the Git Large File Storage system (https://git-lfs.github.com/). Please install this system before proceeding.

Reproducing the results

Note

All the code below were run on a server with 15 cores.

Running the simulations

To reproduce the simulations (Section 5 and Appendix D of our paper), navigate to the simulation folder.

To reproduce Figure 2, run illustration_example.R.
To reproduce Figure 3, run factorization_suite.R and factorization_suite_postprocess.R.
To reproduce Figure 8, run wasserstein_simulation.R and wasserstein_simulation_plot.R.
To reproduce Figure 9 through 13, run factorization_suite_others.R and factorization_suite_others_postprocess.R.

Running the analysis

To reproduce the analysis (Section 1, Section 6, and Appendix G of our paper), navigate to the main folder. From this location, run the following lines in the command window. All the results and figures in these sections are reproduced by running main.R, which calls 7 different R scripts in succession. The figures are produced in the last two scripts, step6_figures.R and step7_figures_embedding.R.